It is a question of time versus cost.
For many "real" projects where your time is not for free, especially when there is no mass production, just a single unique product, it is faster and cheaper to leave the Arduino board in the product and buy a new one for the next project.
No time and cost to design and test a PCB, the system can be updated without having to move the processor. If it is not hobby work (this is not criticism or negative) and there is a price tag on your time then the cost of the Arduino board is paid for in one hour.